BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6236063.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 2,890,468 number of mapped reads = 2,490,699 (86.17%) number of supplementary alignments = 19,433 (0.67%) number of secondary alignments = 0 number of mapped bases = 162,533,004 bp number of sequenced bases = 162,452,020 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 139,361 duplication rate = 4.34% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7609 >>>>>>> ACTG content number of A's = 46,507,435 bp (28.63%) number of C's = 30,233,134 bp (18.61%) number of T's = 50,776,870 bp (31.26%) number of G's = 34,933,035 bp (21.5%) number of N's = 1,546 bp (0%) GC percentage = 40.11% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 1,251,884 number of insertions = 12,838 mapped reads with insertion percentage = 0.51% number of deletions = 47,292 mapped reads with deletion percentage = 1.88% homopolymer indels = 47.19% >>>>>>> Coverage mean coverageData = 0.0525X std coverageData = 0.5099X There is a 4.1% of reference with a coverageData >= 1X There is a 0.81% of reference with a coverageData >= 2X There is a 0.18% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 15414068 0.06184164331530392 0.6275668920424053 chr2 243199373 12162013 0.050008406066079786 0.49557809610759823 chr3 198022430 15283987 0.07718311001435545 0.3429964191732442 chr4 191154276 8618436 0.04508628412790515 0.3129313561175443 chr5 180915260 7417001 0.040997099968239276 0.25081072332632715 chr6 171115067 14436204 0.08436547554284042 0.4365051897848785 chr7 159138663 10613945 0.06669620568572955 0.6003619128530796 chr8 146364022 9624261 0.06575564724505863 1.4566960765021246 chr9 141213431 6879263 0.048715359093569506 0.4106765513935225 chr10 135534747 6418469 0.047356630989985174 0.42425583901120334 chr11 135006516 5582134 0.041347145051872904 0.33439488706880244 chr12 133851895 6131799 0.045810326405913045 0.2732967030311445 chr13 115169878 5801694 0.05037509894731329 0.275680976513824 chr14 107349540 5178926 0.04824357887327696 0.28388981984867506 chr15 102531392 4692913 0.04577049924378282 0.2709264889060603 chr16 90354753 3899619 0.0431589802475582 0.27661836491977443 chr17 81195210 3062418 0.037716732304775125 0.2675522538028424 chr18 78077248 3950610 0.05059873524230772 0.6960316624762829 chr19 59128983 2086662 0.035290003212130334 0.4447736031015778 chr20 63025520 2819959 0.044743129449784785 0.26991482981130105 chr21 48129895 2639524 0.05484167376637743 0.31386176783316816 chr22 51304566 1615200 0.0314825779834099 0.21294691395020976 chrMT 16571 230856 13.931325810150263 9.565697600140485 chrX 155270560 7559588 0.04868655075372949 0.2909417563113451 chrY 59373566 413455 0.006963620814016797 0.20105159685216928